Doctor Who: And Then There Were Two
by IdrisTheTARDIS314
Summary: On hold for awhile. After the Time War, the Doctor is lost and alone. After the Time War, Rex is left homeless and without hope for happiness. Can he save her from a ghastly band of space pirates before it's too late? And will he ever truly be healed of the hurts he endured deep in the midst of total war? Somewhat AU, set before the Doctor meets Rose. Rated T because I'm paranoid.
1. Chapter 1: A New Begining

_**Chapter 1: A New Beginning**_

I sank to the floor of the TARDIS as the reality of what I'd just done sank in. I'd stopped the Time War. It was over. And the participants killed. All of them but me. What kind of person did this make me? What kind of person was I to do something like that? The Time Lords and the Daleks, all dead. No survivors. In desperation, I reached out with my mind, looking for someone. Anyone. I found no one. The guilt crushed me from the inside out, preventing me from moving from the spot I was in. Tears fell from my eyes for the first time in centuries as I wept for my fallen race.

"What have I done?" I murmured to myself. "What have I done?" I sat there repeating the question for who knows how long? Eventually, a beeping sound emanating from the TARDIS console pulled me out of the fog that had settled in my mind. I managed to pull myself together enough to make sure she wouldn't explode and then sat in the captain's seat. I put my head in my hands. The message on the monitor had said the Time Lock around Gallifrey and the Time War was complete. Not only had I committed genocide on two entire races (with possibly many more dying due to the repercussions), but I had prevented them from ever coming back. The only things that could happen in that time period were things that had already happened. A Time Lock was more effective at making sure history didn't change than the Web of Time.

Through the haze in my mind, I realized that I should probably pilot the TARDIS away from the Temporis system. In fact, I should probably have piloted the TARDIS away from the entire constellation of Kasterborous. I didn't care at the time, though. The disappearance of a planet would cause the orbits of everything in the system to change, maybe even the whole sector of space, but I was too steeped in guilt to care. I just sat there, risking crashing into a stray asteroid or moon. After what felt like days, but was probably just a few hours, I had cried myself to sleep.

A TARDIS quake was what woke me up. For a few seconds, my mind was groggy, but then I realized that the TARDIS was being pelted by small meteorites from the rings of Karn. Why the rings of Karn were attacking me, I had no idea. I just needed to get out of there. I quickly jumped up to the controls, pulling levers and pushing buttons, this way and that. The TARDIS emitted a whooshing vworp sound, like metal scraping against metal, except it was pleasing to the ear. It was a sound that harmonized with the very fabric of the universe. Destination: Earth. Hopefully.

As my grogginess from my unplanned nap slowly disappeared, I remembered why I was in the Temporis system and why the rings of Karn were attacking me. Without Gallifrey's gravity pulling on it, Karn's orbit would slowly send it careening into Temporis II, one of the suns. Of course with my memory, my crushing guilt and sadness came back as well. Tears fell again, but I managed to keep my wits enough to pilot the TARDIS properly… enough. I don't think she liked getting wet, though.

Suddenly, the warning sound started, the one that said something was up with the Time Vortex. I checked the monitor and forgot to feel guilty as I saw what was going on.

"What the hell is that?" I shouted, despite there being no one to shout at. There was a blockage in the timestream. And I was about to crash into it. Terror at crashing in the middle of the Vortex filled me as I started to frantically reverse the trans-directional output. I pulled the override switch for the Dematerialization Circuit and ran halfway across the TARDIS to pull the emergency brake. The vworp immediately became a painful screeching. The combination of the two functions would hopefully be enough to blow the old girl from the Time Vortex back into real space. Either that, or I'd be blown into the Void. She shook around for a few more minutes, then came to a halt, her engine noise dying down as well.

"Well, that was interesting," I muttered. I accessed the temporal scanner controls on the console to try and figure out what had blocked me, but nothing happened, which confused me until I saw that the psychotic evasive maneuvers I had performed had drained the TARDIS' power. I would need to wait until enough could be generated from the Eye of Harmony to pilot back into the Vortex. The guilt tried to come back, but I pushed it away. Thinking about it would just reduce me to being useless again, and that couldn't happen. Of course not thinking about it wouldn't work 100% of the time. I needed to find a way to ease it so it wasn't so overwhelming. I needed to help people again. Maybe I wouldn't be able to make up for what I'd done, but maybe I could at least try. Especially if it would make the guilt go away.

I made up my mind then and there. I would do what I was best at, helping people whether I wanted to or not. Even if I couldn't truly redeem myself for what I'd done, I could sure as hell try.

**Author's Note: Hello, Idris here. The idea for this story has been mulling around in my head for a really long time, so I finally got around to writing it. I have all sorts of other stuff going on too, so don't expect regular updates. The story is going to go all the way to the 12th Doctor (although probably not all in the same fic) before getting super AU other than Rex, so I hope you guys stick with me. Please review so I know if I'm doing something wrong because this is my first Doctor Who fic. Especially if it's a continuity error that I didn't put in on purpose. I can't stand those. Anyone who reviews gets an internet cookie unless the reviewer is flaming. I don't like flames. If you have a problem with the way I write and feel the need to make a huge deal out of it in an insulting way, then there's a simple solution to that. Just don't read the fic. Thank you :)**

** -IdrisTheTARDIS314**


	2. Chapter 2: The Lonely Planet

_**Chapter 2: The Lonely Planet**_

As soon as I made up my mind about what I was going to do with my life, I remembered to do a full body inventory. I made sure I still had a head, arms, legs, etc… You never know what Regeneration is going to give you, at least when you're me without the Sisterhood of Karn. When I was satisfied that I had all the required body parts, I smiled. Nothing had gone wrong. Something was odd, though. Not about myself but the TARDIS. Something was different, and I couldn't seem to place it.

Suddenly, I felt a shooting pain in my head that left after a few seconds. Brilliant, my Regeneration side effect would be headaches. Well, it would be better than amnesia or fainting. I'd experienced those one too many times. Turning to look at the door, I decided to check what was outside. Doing so would help me to figure out where I was.

I stepped out of the TARDIS, unsure of what to expect. Emergency landings are always annoying like that. Almost immediately upon exiting, though, I descended into fits of coughing. This wasn't a Regeneration side effect, as I could smell the acrid odor of salicylic acid permeating the air. Pure poison to Time Lords. I stumbled back onto the TARDIS and took long, deep breaths once I was sure I wasn't in the acid filled atmosphere anymore. I hoped that I hadn't breathed too much in. Knowing how fast Aspirin poisoning had nearly killed me once, I fumbled for the type 4 emergency compartment under the console. Sure enough, it had a few pieces of chocolate. I ate a piece and waited for it to take effect before trying to move.

"Fantastic, just fantastic," I muttered, my voice oozing with sarcasm, "I'm stuck on some random planet for who knows how long, and of course the air's unbreathable." I breathed in and out to calm down. Getting mad would do me about as much good as getting sad. Pulling the monitor over to the keyboard, I looked up a list of planets with salicylic acid naturally occurring in their atmospheres on the TARDIS Data Core. Once I had the list, though, I pulled the factual data from my own personal knowledge.

Adipose IV: The 4th planet of the Adipose system. Covered in colorful forests and oceans teeming with life.

Coelozyca: 2nd planet in the Physis system. Colonized by Silurians trying to escape a disaster on Earth that never actually happened.

Klom: Same system as Raxacoricofallapatorius. Home to a race of creatures that absorbed other life forms to feed off of their emotions and experiences.

Nandarin III: 3rd planet of the Nandarin system. A gas giant twice the size of Sol V.

Midnight: 4th planet of the Xenis system. The sun, Xen, radiated deadly X-Tonic ultraviolet rays, making the planets barren of life. Almost completely made of diamond, including the rare Midnight Star diamond.

Polarfrey: 5th planet in the… next planet.

Io: One of the moons of Sol V. Covered in volcanoes that spew sulfuric and salicylic acid rather than lava.

The 4th moon of Poosh: One of the moons of a planet called Poosh. Barren and hostile to all life but not unlivable.

I immediately ruled out Midnight, due to its deadliness, and Nandarin III, due to its gas giant...ness. The planet I didn't want to think about was also a gas giant. It couldn't be Klom or Coelozyca due to the fact that I couldn't see any cities out the window. A forest ruled out Io and the 4th Moon of Poosh. The only planet it could be was Adipose IV. It was most likely before the Adipose had started to colonise it as well.

"Well no point in staying here. I'll just get bored," I said to myself. Boredom could lead me to think about things I shouldn't be thinking about. Which would be bad. I went into the hallways of the TARDIS to try and find something that would help me to breathe. I managed to find a SCUBA tank fairly quickly in one of the many appearing and disappearing storage rooms. It was full, so it could last upwards of twelve hours for me if I was careful. Fantastic. Plenty of time to leave, explore a bit and get back. It only took a few minutes to find the remaining parts and set it up. I slung the tank over my shoulder and put the mouthpiece in my mouth as I left the TARDIS again. A twist of a valve started the air release.

Once I was out, I spun around to look at my surroundings. The TARDIS had landed in a large clearing. My eyes stung a bit from the acid in the air, but as long as I didn't breathe it in or ingest any, I would be fine.

The forest itself was beautiful, the leaves on the trees being just the right shades of greenish grey to glow silver in the sunlight. Their trunks not just brown but dashed with bits of gray, black and purple. Many of the bushes close to the ground had a yellowish hue to them. It didn't make them seem sickly, but it instead made them seem to be golden from the same light that made the trees silver. Rainbow hued nuts and berries of every kind adorned the flora. All of this color was possible due to one little pigment called Roygbiv, after the Earth acronym for the colors of the rainbow (or at least the ones the humans could see). The pigment changes color based on how much direct sunlight it's getting, but it only works for certain types of sunlight. For instance, the X-Tonic rays of Xen or the Ultraviolet B rays of Sol Alpha would… oops. I was getting off track. I walked a bit and an uneasy feeling rooted itself in my gut. Something was wrong here. Something I couldn't quite put my finger on. Almost like in the TARDIS, where I couldn't figure out what had changed.

Blinking to try and clear my eyes of the burning acid, I made my way through the forest. No point in coming out here if I wasn't going to explore. The more I walked, the stronger the feeling of wrongness got. I finally decided to sit down and just listen, allowing my senses other than sight to tell me what they saw. My eyes closed, the forest surrounded me. A light breeze blew from what seemed to be westish. It was cool; the season was probably early autumn or mid-spring. The sunlight filtering through my eyelids took on a red color. Silence pressed around me.

I suddenly opened my eyes. Of course. It was the silence. The lack of noise. Adipose IV should be teeming with life, so why couldn't I hear a thing? I stood up and started to pace a bit, my footsteps reassuring me that I wasn't going blind.

_Why isn't there any noise? _I thought to myself. I pulled out my Sonic Screwdriver and scanned the area. Or tried to. It had started to malfunction slightly when I was thrown around the TARDIS in the Battle of… new train of thought. The scarlet light at the end of the Sonic flickered as I tried to scan the area as if taunting me. After a few minutes of whacking it with my hand and muttering to myself, I finally got feedback from it. Results: Zilch on life signs other than myself. Of course, since it was malfunctioning, the results could be wrong, but they were discouraging nonetheless.

I started to make my way through the forest again, periodically attempting to scan for life signs. No matter how far I walked, though, there was nothing. Maybe all of the animals had been driven into the Transillan caves for some reason. With that in mind, I started checking the trees for Transillan settlement signs. The Transillans were a peaceful, bird-like race who devoted their lives to helping other races. Anyone who crashed or needed assistance would find a place with them. They also left carvings on the trees to help people find the caves they lived in. I almost laughed. Bird-people living underground. A comical thought.

Before long, I found one. It looked like a spiral made of feathers. The direction the inner point was pointing would be the direction I had to go. I followed it and a few others I found to the home of the Transillans. The cave entrance was in the ground but was lit from below. I'd met them once before a thousand years or so in their history. For me it was quite a bit less than that, though. They had been a fierce warrior race, willing to do anything to protect their colony groups. They had still been fairly friendly to those who weren't hostile and made a mean Adiposian Ale.

"Hello," I called into the hole in the ground, pulling the mouthpiece to the SCUBA gear out of my mouth. "Anyone home?" I quickly popped it back in. Thankfully, I had remembered not to breathe in while it was out. A bit of motion seemed to erupt out of the corner of my eye, but when I turned to look, there was nothing.

"Hello?" I called back down briefly, worried that no one was down there. After a brief argument with myself ("But they might need help" "But it's none of my business" "But I need a place to stay until the TARDIS is charged" "But I can stay in the TARDIS" "But they might need help"), I started to climb down, the dirt entrance. Soon, though, the rough dirt changed to smooth stone, and the cave opened out into a large cavern.

I spun around to survey the area. I was in what would normally be the main living area, where the Transillans mingled when they didn't have anything to do. It was huge, around the size of two Earth city blocks cubed. There were mats on the floor for sitting and resting, and there were torches on poles lit periodically. The fire provided a warm glow and some much needed white noise.

"Hello?" I called again. I risked trying to take a small breath of the cave air. It didn't sting my eyes, so the acid content couldn't be enough to hurt me. I knew that Salicylic Acid irritated the Transillans respiratory systems as well, so they filtered the atmosphere within their settlements.

Deeming the air safe to breath, I turned a few valves on the oxygen tank to stop the airflow from it. I looked around the cavern again. Other than myself, it was devoid of life, almost like a banana peel with all of the… wait… that was a horrible analogy. More like a house that had been abandoned by its owners. I frowned upon my analogy making skills. The first one made no sense in the context and the second one was boring.

There were several smaller tunnels that branched off from the main one I was in, and I made my way to one of those. It was also lit by torches. I touched the smooth stone wall. It was cool. The entire place confused me. Why did it seem so abandoned when the torches were still lit? There had to be someone here.

Suddenly, I heard a high, screechy sound coming from behind me. I spun around to see a Transillan. He was about 4 feet tall and wore a long robe, almost like a human monk. His head seemed to be like that of a harpy eagle. He made the screech that made up the majority of the Transillans' language, Teriss, again. He was asking who I was.

"Do you understand Galactic Basic?" I asked.

"Yes," The Transillan screeched. I was slightly confused, though. Why hadn't the TARDIS translated for me? She should be right on top of that kind of thing. I had to rely on my own background knowledge of Teriss to understand it, though.

I started to speak in Galactic Basic, "I was just looking for a place to stay while my ship is recharging. I'm sorry if I'm intruding on anything."

"That is quite alright. We always allow for wanderers to stay. Follow," he said. "I am Fen." he motioned for me to follow him. Fen led me through winding hallways and twisting corridors. I made sure to remember the exact direction and location of each, in case I needed to run from something quickly. As we walked, I wondered why the Translation Circuit wasn't working. I tried tracing my telepathic connection to the TARDIS back to her, but it wasn't working. I couldn't tell where she was just by thinking about her like I usually could. Only two things could sever a connection between a Time Lord and a TARDIS. One would be either the Time Lord or the TARDIS dying, which couldn't have happened as nothing could get into her. The second was a Psychic Dampener Field. The second option didn't exactly sever the connection, though. Just suppress it.

"Why is there a Psychic Dampener Field around the area, Fen?" I attempted to mimic the high screeches that made up Fen's name rather than the translation, but all I did was hurt my voice.

"I am not sure what you mean, Doctor. Not being telepathic ourselves, we wouldn't be able to tell if there was such a field or not," Fen told me. "And please, don't attempt to use our language if it hurts your voice as much as it sounds like it does. We'd rather you translate than hurt yourself."

"Thank you," I said, rubbing my throat. My voice wasn't designed to go higher than a certain pitch. It was annoying.

Most of the corridors Fen led me through were empty, but I saw a few other Transillans roaming. I saw a group of five of them surrounding what looked like a closed off area. I thought I saw a flash of movement out of the corner of my eye when I passed them, and turned my head to look. Just like before, when I was debating going into the cave, there was nothing.

Finally, Fen led me into a room about a fourth of the size of the main entrance area. It had a much lower ceiling, though. There were about eighty Transillans milling around, seemingly off duty. Fen had told me that these were the majority of the remaining Transillans in this particular forest. There used to be thousands in this colony alone. That in particular stayed with me. Whoever or whatever had killed them had achieved near genocide.

Fen led me to an older looking Transillan who looked a bit like an owl sitting near the center of the room. I greeted him with the traditional Transillan greeting. Or I hoped it was in this period of time. It required me to touch the tips of my right index and rings fingers and splay out my thumb and pinky over my left side.

"You know our customs young one?" the Transillan asked.

"Yes. I've been here before, and I'm anything but young," I said with a slight smile.

"Then you just look the part of a youngling," he concluded. "I am Rako, the colony elder. What brings you here?"

"I may have slightly crashed my ship, and her battery will take awhile to recharge. I need a place to stay until then," I answered.

"You are perfectly welcome to stay with us, but I must warn you. We are constantly under attack by sky warriors," Rako said. I abruptly stopped moving when he said that. Sky warriors was about as close as they had within their language to space pirates. The Transillans hadn't even developed their own space travel yet. Could this be my first chance to help someone?

"I can help with that," I could hear the desperation in my own voice.

"No. This is our problem to take care of," Rako seemed determined not to allow my help. "You should rest until your ship is fit for flight." I tried to protest but Rako cut me off. "Fen and Sola will show you to a room. We do not really have much in the way of privacy, though."

"That's alright. I was never much one for privacy anyway," I started to follow the two Transillans away.

"Says the man who will not reveal to us his name," I heard Rako say behind me. I stopped for a second. My name. Who was I now? I wasn't the Doctor, that's for sure. Not after… new train of thought. I left the room with Fen and Sola, trying (and failing) to think light, fluffy thoughts.

**A/N: Hello again. I haven't recived any flames yet, so that makes me happy. On the flip side, I haven't gotten any reviews yet either, so that worries me. Was the beginning so bad that nobody even wanted to bother? I hope not. I know I shouldn't be worrying because this is only chapter 2, but I'm super paranoid. **

**-IdrisTheTARDIS314**

**P.S. I apologize for any distress my author's note may have caused. Anybody can totally skip reading them. I won't be sad. In fact, I will completely understand because I tend to rant sometimes in Author's Notes.**


	3. Chapter 3: Discovery

****A/N: Hello. I apologize in advance for the stupid computer meme reference. My brother bet that I couldn't find a place for it in this fic, so now he owes me 5 bucks.********It also made it so that I had to make this chapter a bit weird, though, so sorry. Also, Sylphs are a Gallifreyan system of measurement that I made up. One Sylph is about equal to 2 inches (or 2.14 inches to be exact). That makes 31 Sylfs 66.34 inches or 5 feet and 6.34 inches. That'll make sense later. Lastly, I apologize for a possible bad character description. Enjoy the chapter.****

****-Idris****

_**Chapter 3: Discovery**_

Two weeks. Two weeks of headaches and abnormal sleep patterns. That's how long I had been with the Transillans, and the TARDIS still wasn't finished charging (I had been making regular trips to check up on her). Whatever was wrong with the Time Vortex was keeping her from charging properly. At least there was enough power to work the Temporal Scanners. The bad news was that even the TARDIS couldn't figure out what had gone wrong. The other bad news was that the Transillans still weren't letting me help them.

"Are you sure I can't help," I had reduced myself to bugging Rako constantly.

"No," the bird replied tersely. His patience with me seemed to be wearing thin. Needing to sleep much less than the Transillans, I used the nighttime hours to investigate anyway, but I didn't want to meddle where I wasn't wanted.

"I can take my ship up to have a chat with them," I suggested. The TARDIS had enough power for that at least. I just couldn't get her into the Time vortex yet.

"I thought you ship was incapacitated," Rako pointed out.

"She doesn't have enough power for a long enough trip to get… home," I hesitated a bit on the word "home", "but there is-" a large boom and a small earthquake cut me off.

"Not again. You want to help? This is your chance. Warn everyone that a raid is coming," Rako told me. Of course, being me, I didn't exactly listen to him. I hurried to the room I had been assigned, grabbed my oxygen tank and ran out to get to the TARDIS. If I could do this while the Transillans were under attack, they might never know. What was annoying was that I had to dodge ginormous hydrofield lasers. That was technology only the Daleks… new train of thought. It only took me a few minutes of weaving through giant lasers to get close to the TARDIS. At least she wasn't in any danger.

Once inside, I ran to the controls. I hadn't flown her like a normal ship in a long time. Quickly, I made sure that the Gyroscopic Stabilizers and the Thingamawhatsists (I didn't know what else to call them) were on.

"Here we go!" I shouted as I took off. It was strange with the TARDIS shaking around and no Time Rotor running. Coupled with the difference in the atmosphere that I still couldn't place, it made me slightly nauseous, but I managed to keep my lunch. Mostly. I piloted around the lasers as the TARDIS kept going up and up and up until I was about 100 yards away. That specific number of yards because, with the amount of power available at the time, that was the exact range of the Circuit. Obviously not enough power to get into the Time Vortex.

I input the coordinates and pulled the lever for the Time Rotor to start. The familiar vworp filled the air as the TARDIS dematerialized and then re-materialized inside of the pirate ship. I peeked out the door just to make sure there was a viable atmosphere within the ship first. For all I knew, it was piloted by robots. Viable atmosphere: check. I was in luck.

I exited the TARDIS onto the deck, patting my pockets to make sure I had my Sonic Screwdriver. Faulty as it was, it was still quite useful.

"Now which way do I go?" I muttered, looking around for some indication of where to find the bridge. Voices coming from my left prompted me to search for a hiding spot. The best I could do was stand behind the TARDIS, though. Based on their voices and footsteps, there were two of them, and they seemed to be some sort of male humanoid species.

"What the fuck is that?" asked one of them once they got close enough to see the TARDIS. He was speaking in a very bad American accent and seemed versed in the colloquialism of Earth.

"It looks like a Police Box from the 1960's," answered the other, who wasn't masking his natural accent under a bad Earth one. I wasn't sure where the accent was from, though.

"Maybe it is a Police Box from the 1960's," the first guy said. He came around the box to see me in my not so great hiding place. It took me about half a second to see that I was right in my original assessment of them. Their human appearance helped me rule out a large number of species. Unless, of course, they were using some sort of a Perception Filter or perhaps a Shimmer.

"Hello!" I gave them a huge smile. "I was wondering when you guys were going to find me. Hide and seek isn't a game that's supposed to take four hours." I tried my best to sound like I was scolding the, cheerfully.

"Huh?" the first guy went. He seemed to be about 5'7" and had a very stocky build that didn't go well with his light blonde ponytail.

"Precisely," I said as I darted off between the two. Sadly, I didn't last long before the second man caught up to me. He was taller and thinner than his friend with much darker hair. He grabbed onto my arm and gave the shorter man enough time to catch up and grab my other arm.

"Who are you?" the shorter one asked.

"I'm guessing it's a bit too late to whip out the psychic paper and say that I'm a health inspector," I said, despite the fact that I hadn't actually used psychic paper since my second incarnation. In response, the shorter one pulled me away from the other and twisted my arm behind my back.

"Ow. OW! OK, OK. OW!" I shouted. He let up the pressure a bit, "I'm a trespasser trying to figure out your diabolical plans. Take me to your leader." a pause "Please," I added with a large grin. The taller guy shivered a bit when he looked at me.

"Nutcase," he muttered.

"Hey!" I protested.

"Come on, Jak. We'd better take him to the captain,"

"Gotcha," said Jak. He then released my arm enough for me to stretch it out a bit. Then both men herded me in the direction they had come from.

"Oi. No need to be so pushy," I complained. As the two men brought me to what I presumed would be some sort of holding cell, I memorized the layout of the corridors, so I could get back to the TARDIS quickly after my mission was over. After a few minutes of walking, they threw me onto the deck of what seemed to be the bridge.

"OW!" I shouted again.

"We found an intruder, captain," Jak said as I got up from the ground. His bad accent grated my ears.

"Good, thank you Jak and Rax. Now both of you back on patrol. I'll make sure to increase both of your rum rations later," said a man who was presumably the captain of the vessel.

"Got that," the two grunts said together. They were trying to sound stoic, but their smiles betrayed their true feelings. Everyone knows how much spacefarers love their rum. They left the room with those huge grins plastered on their faces (I really hope I don't look like that when I smile). I quickly looked around the room. There seemed to be only one person per essential system. Those people were sitting at stations. Others were standing in animated conversation. This was a pirate ship all right, disorganized and fun.

"IMA FIRIN' MAH LASERS!" the weapons specialist was yelling as the communications specialist tried to calm him down from the seat beside him. He was repeatedly jamming buttons like a four year old (or like me). That was about as much as I had time to take in before the captain grabbed my attention.

"John, shut the hell up. I have an interrogation," the captain said the the overly bouncy crew member who immediately became calm enough to function properly.

"Human crew. Raised on Earth but with knowledge of aliens specifically for the purpose of joining this crew. Parental units probably some sort of humanoid alien. Impressive," I said.

"How did you know that?" the captain asked.

"I didn't. It was a guess, but I'm very good at guessing. What I don't know is why you'd be attacking the Transillans, though," I answered.

"I'm Captain Sturgo Mail. You will tell me your reason for being here or else," he demanded.

"Fun. Isn't that always the case? Although I wouldn't be sad to find out what's so bad about the Transillans that you had to kill them all," I answered.

"How did you get onto my ship?"

"The blue box,"

"Don't play games with me," Captain Mail was starting to fume.

"I'm telling the truth. If you send one of your men to check, you'll find a large, blue police box in your cargo hold. That's how I got in," I said, smiling. This was actually kind of fun.

"Captain, he's not lying. Our security cameras picked this up about half an hour ago," a lady by the door said. She pulled up a video sequence showing the TARDIS materializing and then me coming out. "our scanners have proven what the visual and audio evidence suggests. The blue box is a TARDIS."

"Time Lord," Sturgo spat at me, slight fear evident in his voice. Everyone in the room either stepped or scooted a few inches away from me.

"Nice to know I'm loved," I muttered to myself. What did people have against Time Lords?

"The masters of time who may destroy the universe as we know it," Sturgo kept on talking. Right… that was what people had against Time Lords. Rassilon had just gained approval for the Ultimate Sanction when I activated the Moment. A wave of guilt washed over me as my thoughts strayed to the war. Guilt mixed with sadness. This time I didn't push them away as tears threatened to fall once more. 2.47 billion children who didn't need to die.

"Well lucky you. The war is over," I said. I could hear the bitterness in my own voice, "and the Time Lords are gone."

"What? Then the Daleks won?" Sturgo asked. I could see him slowly backing away from me.

"No. There was no winner because all of the participants are dead. Time Lords and Daleks alike burned alive in the destruction of Gallifrey,"

"They're dead? All of them? How do you know?" Sturgo sounded very scared by this point.

"Because I saw them burn," my voice took a very dark tone. "In fact, I was the one who made them burn!" I let myself feel what I had been pushing away for the two weeks since I had done the deed. All of the guilt, the rage, the sadness, the self-loathing and even more emotions I couldn't even name using most Earth languages. I let myself remember the Moment and how I had felt pressing that big red button. The fear and doubt beforehand. Then a surge of such an immense powerful feeling as I pressed it, as if the universe was mine to control and mine alone. I felt amazing for a fraction of a second before the realization of what I had done sank in. Ever hear of dying of guilt? Well apparently that's possible.

I grabbed my Sonic Screwdriver from the inside pocket of my jacket and pointed it menacingly at the crew. Of course it wasn't actually a viable weapon, but there was no need to tell them that. By this point, everyone in the room had backed up against the far wall, about as far away from me as they could get. You could smell the terror in the air… as long as you were a species with an advanced olfactory system (like Time Lords)

"So, who's planning on getting in my way when I ask why you killed the Transillans, and who's planning on telling me?"

No one else said a word. They were all scared like little children having a nightmare. Even Captain Sturgo was quaking in his boots. I could hear that the lasers had stopped. The systems must've been set to automatically shut off if there was no one manning them. It was utter silence as I walked closer to the terrified group. Interesting how easily one Time Lord can reduce a group of hardened human pirates to crying little sissies in the space of a few seconds. They must've grown up on stories about the horrors committed by my kind.

"Who's gonna answer me?" still no one spoke. "Tell me why you were attacking a defenseless level 3 planet with intent to kill." I waited a few moments for an answer, still pointing my Sonic menacingly.

"The Transillans have our target Mister… uh…"

"Doctor. I'm the Doctor," I said, and I realized that I meant it. The Doctor wasn't just something I called myself. It was a promise. A promise that I had broken in my previous incarnation when I made the decision to fight in the Time War. But no matter what I had done in the past, I would keep that promise now. I would be the Doctor. I looked straight at the young boy, he couldn't have been more than sixteen years old and wasn't even the youngest in the room, who had been brave enough to answer me as a collective gasp came from the rest of the pirates.

"What do the Transillans have that you seem to need so badly?" I asked him, finally lowering my arm.

"A-a girl, Sir," he answered. "She ran away from the Daleks, and they paid us to get her back. We chased her to this planet where she crashed, but the Transillans wouldn't let us have her. They said she was hurt too badly. Then Captain Sturgo gave the order to fire on the Transillans periodically until they gave up," I realized that this was the same boy who had been shoop-da-whooping (is that even a word?) earlier. He looked terrified, and I immediately felt bad for scaring him and all the others. "Please don't hurt me. I was only following orders."

"'I was only following orders,' the motto of the human race. You fight so hard for your own freedom, yet once a real decision has to be made, a life or death decision, you're perfectly willing to pass it off as 'only following orders,' the very opposite of freedom," I muttered. "And what do you know about the Psychic Dampener Field around the area?"

"That was us, too. When the girl crashed, we sent down a Parasite Drone into the wreckage. It had the emitter attached to it. We were hoping that, if she was knocked unconscious by the crash, it would keep her from waking up, which would make it easier for us. We weren't counting on the Transillans rescuing her. The drone is small enough that they probably wouldn't be able to find it," he said. A Parasite Drone. Little robotic drones that latch onto the closest living being (plants, fungi and microscopic organisms not included) and hold on for dear life. I just needed to know the answer to one more question before I had to leave.

"Do you even know what her name is?" I asked.

"N-no. The Daleks didn't say. They just told us to get her, and we didn't ask," he still looked scared, even though I'd calmed down. I had all the information I needed, so it looked like it was time for me to vamoose. I started to turn away but then turned back. Maybe one more thing.

"Since you humans are so fond of your freedom of choice, I'll give you some. Choice A is to stay here and help the Transillans rebuild. Choice B is to remain how you have been and face the wrath of a Time Lord. Choice C is to run far far away and hope I never find you again, you got that?" I got a lot of scared nods. "Alright then. I hope you choose well." Then I left the room and ran as quickly as I could back to the TARDIS. I hoped I remembered the corridors correctly in my mess of emotions. Mess, understatement of the year. It felt more like someone was taking my emotions and sending them through a shredder that had been tossed in a tornado. Everything that I hadn't allowed myself to feel had come pouring through the floodgates I had built. I didn't even know how I felt at that time, my feelings so mixed up that I couldn't separate one from another. I focused my thoughts in one goal to get myself on track. Find the girl and save her. Then I would deal with the pirates if they refused to leave.

When I got to the TARDIS, it took me a minute to get the key in because my hands were shaking so much. The pirates' ship was coming back to life around me, hopefully to do something other than shoot at innocent bird-people. Slight vibrations and movements, undetectable to most species, caused my nausea from earlier to come back. I made it onto the TARDIS, and a reassuring touch brushed my mind. It felt good to be able to feel her telepathically again. She might not be able to communicate in words, but all that needs to be said can be said through feelings.

"Hey old girl," I said to her. I never gave her enough credit. She helped me through so much, and I couldn't even figure out what she'd changed. I went to the console to set the Dematerialization Circuit to as far away as the meager power supply would allow. As she left the corporeal universe, I lost myself in the sound of the universe singing. A sound that can only be heard with the flight of a TARDIS.

I was shaken out of my reverie as the TARDIS came back into space. The violent shaking threw me across the console. I flipped a few switches, hoping the manual flight controls were still working properly. They were but barely. I managed to come to a relatively non-crash type landing. A few trees were now free of leaves on the tops, but I considered it nonconsequential given the circumstances. I grabbed my SCUBA tank from where it had rolled by one of the corridors and hopped out of the TARDIS. My landing site was close enough to the Transillans' cave that it only took a few minutes to get there, as opposed to the two hours of my original point. Once inside, I ran into Rako. Literally. Both of us were knocked to the ground.

"Erm… uh… sorry," I said, holding out my hand to help up the Transillan.

"That is quite alright," he stood up without grabbing my hand and dusted himself off. "Why are you in such a rush?"

"I need to see the girl," I said.

"What girl?"

"The one you're hiding from the pirates. I'm guessing she's in some sort of coma and won't wake up. If that's so, I've found out why," I said.

"Wait. How did you find out about her?" Rako seemed very confused.

"I went to… have a little chat with the pirates. They shouldn't be coming back for awhile. I think I scared them off," it took me a second to find a good word for terrifying them nearly to death.

"Oh… um… why do you want to see her?" he asked.

"Because if she's hurt or anything like that, I can help her. I want to help. Please," I was back to begging. Again.

"Follow me then," he started to walk away, and I came up close behind. The area he led me to was the area I had noticed had a large group of Transillans that seemed to be guarding it.

"Wait," one of them said.

"It is alright," Rako told her. "he is with me."

"Hi," I said, waving a bit and smiling. For some reason, they cringed when I smiled, though. I made a mental note to make a mental note to remind me to do something about that. I couldn't go around with a creepy grin.

Rako led me through the cloth hanging over the doorway. What was through it was a sparsely furnished room; there was just a bed with a bag next to it really. A young girl was lying in it, in her early adolescence by the looks of it. She was wearing a black, short sleeved shirt and pants. I walked over to her, confused by her appearance because she had a combination of physical traits I'd never seen in any species before. Short, grayish silver hair framed her her face. Other than that she looked human. Even though she was lying down, I could tell she was fairly tall for a girl her age. At least 31 Sylphs. Her features were sharp and hawkish. The tip of a scar came out from under her shirt and stopped about halfway up her neck. And close to that scar was exactly what I was looking for. A small robot that had sharp legs digging into her skin to keep from falling off.

"Well lets get that drone off of you," I muttered, walking over to her. The best way to remove a parasite drone is also the best way to remove a band-aid. Pull it off really fast. Which is what I did. "All better"

"Really?" Rako said behind me.

"Yep. All you needed to do was pull off this little robotic fly type thingy," I held up the drone.

"She doesn't seem to be waking up, though," Rako was dubious. All to be expected from a rather non-technology oriented species.

"It'll take awhile. She needs time to gather her thoughts. And self. And everything else. And when she does wake up, she'll probably be very confused and disoriented. So be careful," I instructed. Then, I went to sit down on the floor next to the bed.

"What are you doing now?" Rako questioned.

"Sitting here to make sure she wakes up alright. I'm guessing she comes from an advanced species, judging by the fact that she was flying a spaceship by herself, but even that is no guarantee of a proper awakening. I'm here to help if she needs it," I smiled, making Rako cringe. Yep. Definitely needed to do something about that.

"Well, I will leave you to your devices" Rako said, and then he left the room. Leaving me alone with an unconscious alien from an unknown species.


	4. Chapter 4: Awakening

_**Chapter 4: Awakening (Rex's POV)**_

When I came back from unconsciousness, it was like waking up a long sleep. A very long sleep. I was incredibly disoriented. The slight motion of the planet spinning was enough to make me slightly nauseous. I pushed that feeling to the back of my mind, though as I opened my eyes, still lying down. The light was dim enough so that it didn't hurt my vision but enough to see where I was. Theoretically. I'd need my glasses first to actually judge that properly. Right at that moment, my vision was too blurry to see much of anything. The general airflow in the room suggested a rather small space, and I wasn't on the floor but elevated a bit. Probably in a bed judging by how comfortable the surface below me was.

Something was wrong, though. My reactions, perceptions, even my thought processes were slowed down considerably from the last time I had been awake. My heart rate seemed to be slowed, too. My internal body temperature seemed to be lower than normal as well, making the air around me uncomfortably warm. My breathing seemed to be faster than usual, though. Not enough oxygen, then. A cardiovascular problem. That wouldn't help me in the long run. Even without the nausea, I felt horrible overall.

Through the discomfort, I felt the air shift a bit and tensed up, noting my slowed down reaction time to the observation. Someone else was in the room with me. Almost automatically, I called up several worst case scenarios, but I stifled that train of thought as quickly as I could. If I was in danger, it wouldn't do me any good to panic.

"Who's there?" I called, getting ready to jump up and run if I needed to.

"Excuse me? What did you say?" a man's voice in a different language than I had spoken in. Gallifreyan. I berated myself for having spoken in my own native language. Almost no one knew it. I should've thought to try and speak something else. But something was wrong. I had understood his words perfectly, and I was barely able to ask someone's name in Gallifreyan. I sat up to try and look in the direction his voice was coming proved to be a mistake, though. A sharp pain shot through the right side of my chest, and I let out a groan. However, I was trained to be able to ignore pain. It wouldn't incapacitate me. My left knee seemed a bit stiff, too, when I tried to cross my legs, but that was easily fixed with some stretching. A blurry figure moved slightly but then stopped as I took a few deep breaths and then resumed sitting up all the way. With that out of the way, I could focus on more important things. The blurry figure was presumably the other person in the room. I could certainly see him but barely, and I couldn't make out any of his features.

"Time Lord?" I attempted to ask with my own halting control over his language. Time Lord, a regenerative species from Gallifrey. Crap. Please not a Time Lord, not a Time Lord, anything but a Time Lord. If he said yes...

"Yes. Oh, you don't actually have to try and speak Gallifreyan. Everything I say is being translated by a psychic field generated by my ship. And everything you say, too apparently, which is odd because you've never been near her before. Are you psychic by any chance? I can't tell because I don't know what species you are, and that makes it rather difficult to judge anything about you. " the Time Lord shot out all at once. Didn't even stop to let me think in between his words, which was probably good. I started to move slowly towards the edge of the bed I was sitting on.

"What?" I asked, trying to give the illusion that I was at ease. I wasn't speaking Gallifreyan anymore but wasn't willing to speak my language again either, so I had decided to settle on a fairly species neutral language. English (with a Scottish accent, always have to be sure of the accent). Origin planet: Sol III, a planet visited and invaded so often that its languages were widely spoken throughout the universe. English itself was almost as common to run into as Galactic Basic, the official language of the Mutter's Spiral galaxy. I just happened to have lived in Scotland for awhile.

"Er… sorry. I do that a lot. Talk nonstop I mean. I'm the Doctor by the way," he said. I involuntarily drew away a few inches as one of the fuzzy blobs in my vision moved towards me. A wall against my back made me a bit nervous. What if I needed to run away? That limited my options a bit.

"Th- the Doctor?" I stammered. Not only did I have the bad luck to be stuck in a room with a TIme Lord, but I was stuck in a room with this particular Time Lord.

"I'm guessing you've been raised on stories about the Big Bad Doctor, too. Seems like half the universe has by this point. Whatever you heard, I'm probably not that bad," he seemed like he was trying to reassure me. Hearing about him in children's stories, that's what I'd call being afraid of the Doctor. I squinted to try and bring my vision into focus, but it didn't work. Still too blurry to see much of anything.

"You're a Time Lord. The Time War. You must be a warrior. A soldier. All of the Time Lords are," I managed to get out most of my explanation.

"Oi, no need for the Time Lord stereotype. Just so happens that the war is over. I'm peaceful," he said. His voice dropped slightly as he spoke, like he was sad. I was almost certain of that, but I could also detect the barest hint of another emotion there. It was slight, but it was there. Grief maybe? Or guilt…

"Over? But… who won?" this was news. I had come to this planet… how long ago? In fact, the best inference I could come up with for my general location was somewhere in the Adipose system. At least that's where I'd crashed. Oh! The crash! I lowered my head and grabbed my hair with my hands as the memory of the crash came back. I had been piloting a small, one person craft when it was hit by one of the pirates missiles. After that was a lot of noise, light, pain and fear and then nothing. Everything went blank.

"Are you alright?" the Doctor sounded alarmed. I felt something on my arm and drew away quickly with a small cry. Now I was stuck in the corner. Brilliant.

"I'm fine, I'm fine," I said, pushing away in the general direction I thought he was in. I managed to whack him. Felt like leather. Jacket maybe? He moved away. "Have you seen my travel bag? Did it survive the crash?"

"I'm guessing the you're talking about this," he reached over and dropped something next to me. I grabbed it and started rooting through it. Definitely my bag. The bridge had been shielded enough that both me and my bag survived the crash, so my falling unconscious had probably been from hitting my head. Maybe I should use a safety restraint next time I go crashing a ship. A few seconds later, I managed to snag something that felt like my glasses and pulled them out.

"You wear glasses? I thought that was an Earth thing," the Doctor said.

"I lived on Earth for awhile. Scotland specifically. I guess I never told you my name. I'm Rex," I said, putting on my glasses. Much better. Now I had all of my senses available to me, however muted they may be. I looked at the Doctor. He was tall. Taller than me. Probably six feet or so, which was higher than average for a Time Lord, even after several Regenerations. Despite his assurances, he was definitely dressed like an off duty Earth soldier or maybe a veteran. He was keeping up a color scheme of black, black and more black as shown in his leather jacket, pants and combat boots. He also had very short, brown hair. Military haircut if I ever saw one.

"Well, hello then Rex," he smiled and started to extend his hand to me but then thought better of it.

"You said the Time War was over. Who won?" I asked. Slowly, I started inching myself out of my corner. Being scared of the Doctor wasn't going to do me any good. Even if he did turn out to be bad. Especially if he turned out to be bad.

"Nobody won," he seemed to get sad again. Not just sad but several different emotions. Anger, grief, guilt. The list could go on.

"A stalemate?"

"No. Not that. There aren't enough left of either for there to be a stalemate," he said.

"So the Daleks and Time Lords finally destroyed each other. A war that big, it was bound to happen," I tried to imagine how few of a species you'd need for there to be too few for a stalemate.

"Yea," the Doctor started to space out. It was almost as if he was looking at something that wasn't there. He looked up after a second. "What are you giving me that look for?"

"What look?" I hadn't been giving him any sort of look. I think.

"You were looking at me like I was crazy," he accused. Oh. That look. I tend to get that look a lot. No clue why.

"I wasn't giving you a look," I defended. I don't do looks, no matter what anyone says.

"Whatever," the Doctor tried to look nonchalant. Needless to say, he failed. "I'm going to go get something to eat. Follow me if you want."

"Alright," I said as he walked out. Then, I turned back to my bag. A quick search assured me that everything was still there. Except for my staff. Usually it was held to the side of the bag by two loops, but right now it was nowhere to be seen. I'd have to go about replacing it eventually. I pulled a long purple cloth out of the bag and looked around for my coat. Luckily, that wasn't missing. It was hanging off of the end of the bed. I stood up, immediately collapsing onto the ground as a sharp pain sent itself through my left leg, the one that had been stiff earlier. That wasn't good. Pulling up my pants leg, I located the source of the problem. I could see that the flesh around my knee was warped oddly, and there were surgical scars the Transillans had probably given me. I had been shot in the leg, and it seemed the Transillans had removed it. The surrounding tissue and bone hadn't healed right afterwards. Walking wouldn't be a problem in the future. I had just been caught unprepared.

More careful now, stood back up again. then, I went over to grab the coat before putting it on and tying it off at the waist with the cloth. On me, it fell slightly past my knees, and it was mostly black with silver stitching.

I looked down at my feet. No shoes on. I preferred it that way, though. Feet can be as versatile appendages as hands if you knew how to use them properly. Going barefoot gave me more options if I got into a scrape or if my hands were tied up. For example, if I had to fight upside down for some reason or another (not a completely unrealistic situation. I once went to a planet where it was considered rude to walk right side up). Plus shoes are often uncomfortable.

Then, I slung the bag over my shoulder and went out into the hallway, looking around as I went. Even ignoring the pain in my leg, I was limping slightly. An obvious fault that I'd have to fix soon. No danger spotted in the immediate area. One can never be too careful, though, so I extended my mental awareness slightly to see if I could sense life forms in the immediate area. The Doctor had been right about me being slightly psychic. It wasn't enough for me to be telepathic or anything like the Time Lords, but I could tell when other life forms were nearby with one exception.

I relaxed when I didn't sense anyone in my immediate vicinity. People nearby sometimes made it slightly harder for me to function. I didn't relax completely, though. The tunnel was a bit too claustrophobic for my taste. I walked over to a piece of paper that I saw taped to the opposite wall.

To Rex

Instructions to get to the cafeteria

Give me back my psychic paper back after

-The Doctor

I pulled it down and the message changed. Psychic paper. The message would probably change as I got to the specific areas indicated. Now the question was whether to follow it or not. Without it, I'd certainly get lost, and psychic paper messages can't lie, but it could be some sort of trap or something. Sure, it would certainly lead me to the cafeteria, but what else could be waiting there?

In the end, I decided to go. I really didn't have much of a choice, not knowing where anything is and all. The paper now said to turn left and then go straight until I found a fork in the tunnel. Following all of the directions one after another brought me on a winding, twisting way through the tunnels. I memorized the way just in case I needed to make a quick getaway. Most of the tunnel walls were smooth and they were lit by torches. The fire cast flickering shadows across the floors and walls that did nothing to appease my fear of a trap. Once in awhile I'd pass a Transillan, which told me I had landed on Adipose IV rather than one of the other planets in the system. I watched them as they passed, making sure they weren't up to something.

Finally, I made it to the cafeteria. It was a large room with several groups of five or six Transillans each scattered about among long tables with stools along them. The ceiling was much higher than in the hallway, appeasing my trapped feeling. It wasn't hard to spot the Doctor. He was easily the tallest person in the room. It didn't look like he had noticed me yet, though. I walked about halfway to him before a thing happened.

"BOO!" someone suddenly shouted from behind me. I'd like to say that I kept my cool and calmly took care of the situation. Sadly, what I'd like to say isn't usually what actually happens. In reality, I shrieked loudly enough that everyone in the room turned towards me. I wheeled around, trying to calm my frayed nerves. The person I saw behind me was a certain surprise.

"Drew, what are you doing here?" I hissed at the human who had managed to find his way behind me. Drew, full name Andrew Jeremiah Kelter, was the only person I'd ever met that I couldn't sense with my ESP.

"Looking for you of course. Managed to get here by pretending to sign on with the pirates chasing you halfway across the universe. I think they left me here, though," he gave me his infuriating smile that came up in the most inappropriate moments.

"You know better than to scare me like that," I was irritated, close to angry in fact. At least that was better than scared.

"I do? Since when?" he feigned ignorance of my sort of social anxiety.

"Since-" I was cut off mid-sentence by a large boom and the ground suddenly shaking. I screamed again and dove under the nearest table, shouting "Earthquake!"

**A/N: I'm sorry. I'm so, so sorry for making you all wait so long for the next update. I had it done ages ago but, then I forgot to post it. Again, apologies. Thank you all for being so very patient, and I'll try not to do that again. No promises, though. Also, Drew will eventually be explained. I hope I made Rex's paranoia seem believable. **

**-Idris**


End file.
